Ferrari ended both practice sessions in first and second, with the gap to Mercedes reading over eight-tenths of a second after the second practice session.
Hamilton's day was far from smooth as he endured throttle issues during the opening session, however set-up changes in between both outings saw him become more comfortable with the car.
"Obviously not a great start for us in FP1, we had a problem with the throttle and I lost power," Hamilton said. "I was idling with the rpm trying to get it back.
"I managed to fix it with a couple of switch changes. When we went back out we had another problem, that was a bit of a mess. I had a few laps towards the end, but not anything spectacular.
"And then we made some changes, we changed because the set up was quite far off going into FP2. It was feeling a lot better but there's still a lot of work to do.
"I don't know about the gaps, Ferrari looks quite quick, they're nearly a second quicker than us just in a straight line down to Turn 5.
"That's quite impressive, but we'll keep just chipping away at it. We're clearly up in the mix, which is good."
Mercedes' advantage over Ferrari this weekend is set to come in the second sector, where there are more corners and fewer straights.
Hamilton says that his balance was a "nightmare" through the second sector during FP1, however he found confidence in the final session of the day
"It's [the balance] not too bad, it was terrible in FP1, it was a nightmare. This one [FP2], it was quite a lot better," Hamilton stated.
"There are some bumps, like at Turn 9, that has always been there but feel worse and worse each year. But it's a reliability competitive sector for us, it's the last two which are all high speed."
Hamilton added Ferrari holds a clear advantage in sector one, while in the last sector it is "quite close" between the two teams.
Bahrain International Circuit - Winter testing